Re: [Gusdev-gusdev] Postgres GUS Scripts

[Jeetendra S. <so...@vb...>]

Hi Michael,

   Thanks for the updates. After downloading the latest code from the CVS,
I was able to register a couple of plugins successfully. Just a small
change while registering GBParser, I had to comment out 'use
GUS::Model::DoTS::NAFeatureImp' line.

I am trying to run GBParser and am having the following problems :-

--An oracle-specific call setOracleDateFormat() in the run mode of the
plugin was causing problems. (For the time being I have commented it)

--It's having problems inserting rows into the tables. The value '' is
being inserted into the NUMERIC type columns. Postgresql doesn't seem to
interprete this as a null value, but an emptry string.


Thank you once again for your help.

Jeetendra.






>
> All,
>
> I've updated DbiDbHandle in CVS to address the capitalization issue
> (thanks to Angel for the pointer here).
>
> This should then allow plugins to be registered with postgres GUS schemas.
>
> Just to recap:
>
> 1) You'll need to use the latest SQL scripts sent by me on 11/30, and
> the latest CVS (as of now!)
> 2) You'll need to change line 34 of GusApplication such that the
> requiredDbVersion for Core is 3.0, not 3.
> 3) You'll need to manually add rows as outlined in VBI's GUS
> installation document.  In addition, you'll need to add these rows:
>
> INSERT INTO Core.AlgorithmParamKeyType
> VALUES(0,'string',now(),1,1,1,1,1,0,1, 1, 1, 1);
> INSERT INTO Core.AlgorithmParamKeyType
> VALUES(1,'float',now(),1,1,1,1,1,0,1, 1, 1, 1);
> INSERT INTO Core.AlgorithmParamKeyType
> VALUES(2,'int',now(),1,1,1,1,1,0,1, 1, 1, 1);
> INSERT INTO Core.AlgorithmParamKeyType
> VALUES(3,'ref',now(),1,1,1,1,1,0,1, 1, 1, 1);
> INSERT INTO Core.AlgorithmParamKeyType
> VALUES(4,'boolean',now(),1,1,1,1,1,0,1, 1, 1, 1);
> INSERT INTO Core.AlgorithmParamKeyType
> VALUES(5,'date',now(),1,1,1,1,1,0,1, 1, 1, 1);
>
> Thanks,
>
> Mike
>
>
> Jeetendra Soneja wrote:
>> Hi all,
>>
>> The reason that I got errors that I posted earlier was that I did not do
>> a
>> build. I had just created the Postgresql GUS schema and was trying to
>> register the gus application. However, after doing a build, things
>> worked
>> out fine.
>>
>> I would like to list some of the problems that I have faced till this
>> point in using the Postgresql version:-
>>
>> -- The rows included in the script gus-rows.pl need a minor
>> modification.
>> Values in the rows that are being inserted into core.databaseinfo need
>> to
>> be changed. The names of the schemas CORE, DOTS and SRES should be
>> changed
>> Core, DoTS, SRes respectively. Also the values for the version numbers
>> should be changed from 1.0 and 3.0 to 1 and 3 respectively.
>>
>> -- Currently, I am having trouble registering a plugin (any plugin). A
>> number of modules/subroutines are retrieving row as a hash-reference and
>> access a value in a row using key, i.e. column name of the table. And
>> all
>> the keys used in the code are in upper case. This works in case of
>> oracle,
>> however, select statements in Postgresql return all the column names in
>> lower case. Therefore, in this case, it couldn't find the row for ga in
>> the core.algorithmimplementation table (although it's there since I have
>> already registered ga). And when I change the key/column name to lower
>> case in GusApplication.pm code, it worked fine.
>>
>> I would appreciate any suggestion or comments.
>>
>> Thanks a lot,
>> Jeetendra.
>>
>>
>>
>>
>>
>>>
>>>Hi Jeetendra,
>>>
>>>Comments below....
>>>
>>>Jeetendra Soneja wrote:
>>>
>>>>Hi Michael,
>>>>        I am glad that the PostgreSQL version has been released.
>>>>
>>>
>>>This is not an official release!!  These are preliminary scripts, which
>>>have had very little testing and are likely to change in the future
>>>(although probably not significantly).
>>>
>>>
>>>>        I had a question about using it. Could you tell me if any of
>>>> the
>>>>existing plugins (especially those in Common::Plugin) would work
>>>>with PostgreSQL version of GUS ?
>>>>
>>>
>>>No existing plugins have been tested with PGGUS.  Please report any
>>>successes or failures you have to the list.
>>>
>>>--Mike
>>>
>>>
>>>>Thanks,
>>>>Jeetendra.
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>>All,
>>>>>
>>>>>Postgres GUS scripts are attached.  The first, pggus.sql contains DDL
>>>>>for creating GUS tables, indexes, constraints, and sequences.  The
>>>>>second, gus-rows.sql, contains DML for populating the core.tableinfo
>>>>> and
>>>>>core.databaseinfo tables.
>>>>>
>>>>>Consider these early beta-- this is not part of an official release,
>>>>>they've had very limited testing, and they are unsupported.  In
>>>>> general
>>>>>the existing documentation should provide the information needed to
>>>>>create an instance with these and GUS with it, but there are
>>>>> derivations
>>>>>that will be necessary.
>>>>>
>>>>>More information on Postgres and GUS, including an official release,
>>>>>should be coming in the next several weeks.
>>>>>
>>>>>Thanks,
>>>>>
>>>>>Mike
>>>>>
>>>>>
>>>>>
>>>>
>>>>
>>>>
>>
>>
>
>
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-- 
Jeetendra Soneja
Research Associate
Virginia Bioinformatics Institute
1880 Pratt Dr., Building XV
Blacksburg, VA 24060, USA
Phone: (540)-231-2789
http://www.vbi.vt.edu